Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals.
Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals.
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DOI：
10.1186/s12862-014-0162-7
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发表时间：
2014-07-23
影响因子：
3.4
通讯作者：
Du D
中科院分区：
文献类型：
--
作者：
Li XQ;Du D
RNA的多聚腺苷化对基因的功能至关重要，但在大多数物种中，围绕mRNA多聚腺苷酸化[PolyA]位点的保守序列基序(通常称为信号基序或信号基序)、基序位置和丰度以及碱基组成模式仍不清楚。Poly(A)位点选择的进化趋势在很大程度上仍然未知。我们分析了31个种或门的Poly(A)位点区域。不同种类的物种表现出不同的PolyA信号基序：在克氏锥虫的PolyA位点上有UUACUU；在莱茵衣藻中有UGUAAC(在该位点上游约13个碱基)；在人芽囊原虫Poly(A)位点下游的第4个碱基上有UGUUG(或UGUUGUU)；在动植物中在PolyA位点上游的大约16个碱基和大约19个碱基上有AAUAA。多聚腺苷酸化信号基序在聚(A)位点周围通常比在整个基因组中丰富几百倍。根据物种或门的不同，这些主要基序通常有非常特定的位置，无论是在聚(A)位点的上游、在还是在其下游。在所分析的所有物种中，除人芽孢杆菌外，多聚(A)位点通常是腺苷(A)，而在莱茵梭子虫中有微弱的A优势。真菌、动物、植物和致病疫霉原生生物具有“富U-富A-富U-富U-Poly(A)位-富U区”(简称U-A-U-A-U-U)的基本碱基丰度模式(或碱基组成模式)，但不同界别或亚界的碱基丰度有所不同。本研究确定了原生生物、真菌、植物和动物中的Poly(A)信号基序、基序位置和mRNA PolyA位点周围的碱基组成模式，为Poly(A)位点的进化提供了洞察力。
The polyadenylation of RNA is critical for gene functioning, but the conserved sequence motifs (often called signal or signature motifs), motif locations and abundances, and base composition patterns around mRNA polyadenylation [poly(A)] sites are still uncharacterized in most species. The evolutionary tendency for poly(A) site selection is still largely unknown. We analyzed the poly(A) site regions of 31 species or phyla. Different groups of species showed different poly(A) signal motifs: UUACUU at the poly(A) site in the parasite Trypanosoma cruzi; UGUAAC (approximately 13 bases upstream of the site) in the alga Chlamydomonas reinhardtii; UGUUUG (or UGUUUGUU) at mainly the fourth base downstream of the poly(A) site in the parasite Blastocystis hominis; and AAUAAA at approximately 16 bases and approximately 19 bases upstream of the poly(A) site in animals and plants, respectively. Polyadenylation signal motifs are usually several hundred times more abundant around poly(A) sites than in whole genomes. These predominant motifs usually had very specific locations, whether upstream of, at, or downstream of poly(A) sites, depending on the species or phylum. The poly(A) site was usually an adenosine (A) in all analyzed species except for B. hominis, and there was weak A predominance in C. reinhardtii. Fungi, animals, plants, and the protist Phytophthora infestans shared a general base abundance pattern (or base composition pattern) of “U-rich—A-rich—U-rich—Poly(A) site—U-rich regions”, or U-A-U-A-U for short, with some variation for each kingdom or subkingdom. This study identified the poly(A) signal motifs, motif locations, and base composition patterns around mRNA poly(A) sites in protists, fungi, plants, and animals and provided insight into poly(A) site evolution.
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影响因子：
64.5
作者：
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通讯作者：
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影响因子：
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作者：
Du D;Lee CF;Li XQ
通讯作者：
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